maplepath := '${EXECUTABLE_MAPLE}':
datadirname := '${DATA_DIRECTORY}':

assigned := proc( a ) option builtin;  1 end:
traperror := proc( expr ) option builtin;  2 end:
eval := proc( expr ) option builtin; 3 end:
If := proc( cond, exprtrue, exprfalse ) option builtin; 4 end:
time := proc( expr ) option builtin; 5 end:
noeval := proc( expr ) option builtin;  6 end:
evalb := proc( BooleanExpr ) option builtin; 7 end:
return := proc( returnvalues ) option builtin;  8 end:
ReadLibrary := proc( filename, funcname ) option builtin;  9 end:
zip := proc( expr ) option builtin; 10 end:
sum := proc( a ) option builtin;  11 end:
UTCTime := proc ( expr ) option builtin; 12 end:
seq := proc( e  ) option builtin;  13 end:
remember := proc( f ) option builtin; 14 end:
assert := proc( bool ) option builtin; 15 end:
product := proc( a ) option builtin;  16 end:
printf := proc( pattern:string ) option builtin; 50 end:
prints := proc( ) for z in [args] do printf('%s\n',z) od end:
error := proc( errormsgs ) option builtin; 51 end:
iterate := proc( itervalue ) option builtin; 52 end:
lprint := proc( toprint ) option builtin;  53 end:
dprint := proc( toprint )
    for i to nargs do
	if i >= 2 then printf( ',' ) fi;
	printf( '%A', args[i] ) od;
    lprint()
end:

FindLongestRep := proc( db:database, len:{posint,0}, endbonus:integer )
option builtin; 300 end:

Match := proc( MatchParams ) option builtin; 55 end:

max := proc( numbers ) option builtin, numeric; 56 end:

min := proc( numbers ) option builtin, numeric; 57 end:

CreateArray := proc( ranges, inivalue ) option builtin; 58 end:

DrawPlot := proc() option builtin; 59 end:

sort := proc( a:array, orderproc ) option builtin; 61 end:

CreateString := proc( len:{posint,0}, inivalue:string ) option builtin; 301 end:

op := proc( ) option builtin; 63 end:

names := proc( typ:{type,'assigned'} ) option builtin; 302 end:

ReadRawLine := proc( promptstring:string ) option builtin; 316 end:

ReadLine := proc( promptstring:string ) option builtin; 303 end:

CodonToInt := proc( UUU:string ) option builtin; 66 end:

GetAllMatches := proc (m: Match, DM:DayMatrix, goal:numeric) option builtin; 169 end:

sprintf := proc( pattern ) option builtin; 69 end:

NucPepDynProg := proc( nuc: string, pep: string, DM: DayMatrix,
    len1: integer, len2: integer, IntronScoring: list )
  option builtin; 305 end:

append := proc(l:{list,structure,set}) option builtin; 71 end:

TimedCallSystem := proc( command:string, timeout:posint )
option builtin; 307 end:

LockFile := proc( filename:string, message:string ) option builtin; 308 end:

MinSquareTree := proc( Dist: matrix(numeric), Var: matrix(numeric),
	Labels: list, Initial: {Tree,'Random','NJRandom','Trials'=posint},
	Keep:'KeepTopology' ) option builtin; 266 end:
LeastSquaresTree := ":
Synteny_Invert := proc( p:list, i1:posint, i2:posint,
	mode:'InPlace' ) option builtin; 267 end:
Synteny_FindOrders := proc( p:list ) option builtin; 268 end:
Viterbi := proc( seq:list(posint), STS:{list(list(list(numeric))),SparsePFA},
	S:list(numeric) ) option builtin;  270 end:
ViterbiFast := proc( seq:list(posint), STS:{list(list(list(numeric))),SparsePFA},
 	S:list(numeric) ) option builtin;  271 end:
ViterbiFast1 := proc( seq:list(posint), STS:{list(list(list(numeric))),SparsePFA},
        S:list(numeric) ) option builtin;  272 end:
SparsePFA_FixedPoint := proc( seq:list(list(posint)), spfa:SparsePFA )
	option builtin;  273 end: 

CallExternal := proc(prog:string) option builtin; 74 end:

ReadOffsetLine := proc( file:string, ofs:{0,posint} ) option builtin; 196 end:

GetOffset := proc( t:string, df: database ) option builtin; 309 end:


NucPepBackDynProg := proc( nuc: string, pep: string, DM: DayMatrix,
                        len1: integer, len2: integer, IntronScoring: list )
  option builtin; 306 end:

NBody := proc (dist:matrix(numeric), var:matrix(numeric),
	k1:posint, k2:posint, rho1:numeric, rho2:numeric,
	inipos: matrix(numeric))
  option builtin; 310 end:

GetEntryNumber := proc( offset:{integer,string}, df: database )
option builtin; 311 end:

type := proc( expr, typeval ) option builtin; 83 end:

DynProgStrings := proc( m:{Match,Alignment}, dm:DayMatrix, noself:'NoSelf' )
option builtin; 85 end:

SmallAllAll := noeval(ReadLibrary(SmallAllAll)):
AlignOneAll := proc( seq:{string,posint}, db:database, day:DayMatrix,
  cutoff:numeric, entries: posint..posint ) option builtin; 314 end:
Alignment := noeval(ReadLibrary(Align,Alignment)):
Align := noeval(ReadLibrary(Align)):
EstimateLogEvalue := noeval(ReadLibrary(Align,EstimateLogEvalue)):

AToInt := proc( A:string ) option builtin; 100 end:
IntToA := proc( P:posint ) option builtin; 101 end:

AAAToInt := proc( AAA:string ) option builtin; 102 end:
IntToAAA := proc( P:posint ) option builtin; 103 end:

AminoToInt := proc( Amino:string ) option builtin; 104 end:

IntToAmino := proc( P:posint ) option builtin; 105 end:

type_type := proc(t) option internal;
if t='type' then true else a := traperror(type(t,t)); a <> lasterror fi end:
nonnegative_type := {0,positive}:
DNA_type := {'A','C','G','T'}:
RNA_type := {'A','C','G','U'}:

# option zippable can be used for functions which do not have an interpretation
# over matrices (other than zipping through).  E.g. exp(), ln()
abs := proc( x:numeric ) option builtin, numeric, zippable, polymorphic;
107 end:

mod := proc( a:numeric, b:numeric ) option builtin, numeric, polymorphic;
108 end:

iquo := proc(a:integer,b:integer) option polymorphic; trunc(a/b) end:

sqrt := proc( x:numeric ) option builtin, numeric, zippable; 109 end:

exp := proc( x:{numeric,matrix(numeric)} ) option builtin,polymorphic; 110 end:
ln := proc( x:{numeric,matrix(numeric)} ) option builtin,polymorphic; 111 end:
log := proc( x:{numeric,matrix(numeric)} ) option builtin,polymorphic; 111 end:
ln1x := noeval(ReadLibrary(ln1x)):
expx1 := noeval(ReadLibrary(ln1x,expx1)):

length := proc( x ) option builtin; 112 end:

TextHead := proc(x:string) option builtin; 113 end:

round := proc( x:numeric ) option builtin, numeric, zippable; 114 end:

sin := proc( x:numeric ) option builtin,numeric,polymorphic,zippable; 115 end:
cos := proc( x:numeric ) option builtin,numeric,polymorphic,zippable; 116 end:
tan := proc( x:numeric ) option builtin,numeric,polymorphic,zippable; 117 end:
arcsin := proc(x:numeric) option builtin,numeric,polymorphic,zippable; 118 end:
arccos := x -> Pi/2-arcsin(x):

Rand := noeval(ReadLibrary(Rand)):
Normal_Rand := proc( nr:structure ) options builtin, numeric; 88 end:
Graph_Rand := noeval(ReadLibrary(Graph,Graph_Rand)):
SetRand := proc( seed:integer ) option builtin; 120 end:
RandL := proc( x:{list,set,string}) x[ceil(Rand()*length(x))] end:
RandomSelection := noeval(ReadLibrary(RandomSelection)):

OpenAppending := proc( filename:string ) option builtin; 121 end:

OpenWriting := proc( filename:string ) option builtin; 122 end:

GaussElim := proc( A:array(array(numeric)), b:array(numeric) ) option builtin;
123 end:

SearchArray := proc( x, a:array ) option builtin; 124 end:

sequal := proc( a, b ) option builtin; 125 end:

CallSystem := proc( command:string ) option builtin; 126 end:

ReadRawFile := proc( filename:string ) option builtin; 127 end:

Set := proc( Option:{string,string=anything} ) option builtin; 128 end:

parse := proc( x : string ) option builtin; 129 end:

arctan := proc( y:numeric, x:numeric )
option builtin,numeric,polymorphic; 84 end:

log10 := proc( x:{numeric,matrix(numeric)} ) 
t := ln(x);  0.0625*t + 0.0032055180967481723489*t; 0.5*t-" end:

lg := proc( x:{numeric,matrix(numeric)} )
t := ln(x);  0.5*t - 0.05730495911103659264*t; t+" end:

gc := proc() option builtin; 130 end:

member := proc( x, s:{set,list,structure,identical(intersect())} ) option builtin; 131 end:

version := proc() option builtin; 148 end:
copy := proc( x:anything, depth:posint ) option builtin; 317 end:

ceil := proc( x:numeric ) option builtin, numeric, zippable; 132 end:
erf := proc( x:numeric ) option builtin, numeric, zippable; 133 end:

erfc := proc( x:numeric ) option builtin, numeric, zippable; 134 end:

floor := proc( x:numeric ) option builtin, numeric, zippable; 135 end:
trunc := proc( x:numeric ) option builtin, numeric, zippable; 136 end:


sscanf := proc( t:string, pat:string ) option builtin; 137 end:

matrix_inverse := proc( A:matrix(numeric) ) option builtin; 138 end:

transpose := proc( A:matrix ) option builtin; 139 end:

Cholesky := proc( A:matrix(numeric) ) option builtin; 140 end:

erfcinv := proc(y:numeric) option builtin, numeric,zippable; 141 end:
scalb := proc( x:numeric, n:integer ) option builtin,numeric; 142 end:
ilogb := proc( x:numeric ) option builtin,numeric, zippable; 143 end:

ReadDb2 := proc( FileName:string ) option builtin, internal; 151 end:
ReadDb := proc( FileName:string ) global DB;
    DB := remember( ReadDb2(FileName) ) end:

CreateOrigDayMatrix := proc( Mutations:matrix(numeric),
	AaCounts:array(numeric),
	PamNumber:{numeric,1..posint} ) option builtin; 152 end:

CaseSearchString := proc( pat:string, txt:string ) option builtin; 156 end:

GetMostFrequentGrams := proc( n:posint, k:posint ) option builtin; 160 end:

SearchDayMatrix := proc( PamNumber:numeric, DMS:array(DayMatrix) )
  option builtin; 164 end:
SearchDayIndex := noeval(ReadLibrary(SearchDayIndex)):

CreateDayMatrix := proc( LogMutMatrix:matrix(numeric),
    PamNumber:{numeric,1..posint} ) option builtin; 165 end:

SearchString := proc( pattern: string, text:string ) option builtin; 166 end:
SearchMultipleString := noeval(ReadLibrary(SearchMultipleString)):
SearchDelim := noeval(ReadLibrary(SearchDelim)):

EnterProfile := proc( blockname:string ) option builtin; 167 end:
ExitProfile := proc( blockname:string ) option builtin; 168 end:

BToInt := proc( B:string ) option builtin; 170 end:
NToInt := eval(BToInt):

IntToB := proc( P:posint ) option builtin; 171 end:
IntToN := eval(IntToB):

BBBToInt := proc( BBB:string ) option builtin; 172 end:
NucToInt := eval(BBBToInt):

IntToBBB := proc( P:posint ) option builtin; 173 end:
IntToNuc := eval(IntToBBB):

BaseToInt := proc( Base:string ) option builtin; 174 end:
NucleicToInt := eval(BaseToInt):

IntToBase := proc( P:posint ) option builtin; 175 end:
IntToNucleic := eval(IntToBase):

SearchSeqDb := proc( t:{string,string..string} ) option builtin; 176 end:

ProbDynProg := proc (A:array(array(numeric)), B:array(array(numeric)),
      f:array(numeric), w:posint,
      FixedDel:numeric, IncDel:numeric) option builtin; 179 end:

date := proc( ) option builtin; 180 end:
hostname := proc( ) option builtin; 181 end:


ApproxSearchString := proc( pat:string, text:string, k:posint ) option builtin;
183 end:
HammingSearchString := proc( pat:string, text:string, k:posint ) option builtin;
197 end:

GetAllNucPepMatches := proc( npm: NucPepMatch, D:DayMatrix, goal: numeric ) 
	option builtin; 184 end:

AlignNucPepMatch := proc( npm: NucPepMatch, dm:DayMatrix )
	option builtin; 185 end:

FindNucPepPam := proc( npm: NucPepMatch, DMS:array(DayMatrix) )
	option builtin; 186 end:

SearchOrderedArray := proc( x, a:{array,string,structure} ) option builtin; 187 end:

getpid := proc() option builtin; 188 end:
sleep := proc( n:posint ) option builtin; 189 end:
getenv := proc(varname: string) option builtin; 198 end:
setenv := proc( name:string, value:string ) option builtin; 234 end: 

SearchTag := proc( tag:string, text:string ) option builtin; 190 end:
SearchMassDb := proc( p:structure, n:integer ) option builtin; 191 end:

DynProgMass := proc( p:{array, structure}, seq: string, stddev: numeric,
	deb: numeric ) option builtin; 192 end:
DynProgMassDb := proc( p:array, m: integer, term: string, df: database,
	stddev: numeric, deb: numeric ) option builtin; 193 end:

ReadProgram := proc( fname:string ) option builtin; 194 end:
OpenReading := proc( fname:string ) option builtin; 195 end:

union := proc(a:set,b:set) option builtin,polymorphic; 86 end:
minus := proc(a:{set,identical(intersect())},b:{set,identical(intersect())})
option builtin,polymorphic; 201 end:
intersect := proc(a:set, b:set) option builtin,polymorphic; 87 end:

subset := proc(a:{set,identical(intersect())},b:{set,identical(intersect())})
option builtin; 203 end:

OpenPipe := proc (cmd: string) option builtin; 106 end:

hash := proc(s) option builtin; 149 end:
hashstring := proc(s:string) option builtin; 150 end:
has := proc(s,t) option builtin; 153 end:
sha2 := proc(s) option builtin; 154 end:

CurrentOff := proc () option builtin; 207 end:

ConnectTcp := proc (path: string, slave: boolean) option builtin; 208 end:

SendTcp := proc (data: string) option builtin; 209 end:

ReceiveTcp := proc (timeout: {0, posint}) option builtin; 210 end:

DisconnectTcp := proc () option builtin; 211 end:

GetGramSiteScore := proc (n: string, S: GramSite) option builtin; 213 end:

GetGramRegionScore := proc (n: string, S: GramRegion) option builtin; 214 end:

EstimatePam := proc (s1: string, s2: string, DMS: array(DayMatrix))
option builtin; 215 end:

DynProgNucPepString := proc( npm: NucPepMatch ) option builtin; 216 end:

ParallelAllNucPepMatches := proc (npm: list(NucPepMatch),
    dm: {DayMatrix, list(DayMatrix)}, goal: numeric) option builtin; 224 end:

antiparallel := proc (nuc: string) option builtin; 225 end:

NucPepRegions := proc (npm: NucPepMatch) option builtin; 226 end:

lowercase := proc(s: string) option builtin;  228 end:
uppercase := proc(s: string) option builtin; 229 end:
assemble := proc(s) option builtin; 230 end:
disassemble := proc(s) option builtin; 231 end:
display := noeval(ReadLibrary(display)):
symbol := proc(s:{symbol,string}) option builtin; 232 end:
warning := proc(s:string) option builtin; 233 end:

ComputeTSP := noeval( ReadLibrary(ComputeTSP)):

ComputeCubicTSP := proc( Dist:matrix, trials:posint, p1:list(posint) )
 option builtin; 253 end:

ComputeQuarticTSP := proc( Dist:matrix, trials:posint, p1:list(posint) )
  option builtin; 254 end:

Eigenvalues := proc( A:matrix, eigenvects:name ) option builtin; 252 end:

VertexCover := proc( A:Graph ) option builtin; 255 end:

VertexCover2 :=  proc( A:Graph, k : integer ) option builtin; 256 end:

CliqueK := proc( A:Graph ) option builtin,internal; 257 end:
Clique := noeval( ReadLibrary(Clique)):
MaxEdgeWeightClique := proc( A:Graph ) option builtin; 265 end:
MaxCut := noeval( ReadLibrary(MaxCut, MaxCut)):
MinCut := noeval( ReadLibrary(MinCut)):
MinimumCut := proc(g:Graph,trials:posint) option builtin; 274 end:

factorial := proc(n:numeric) option builtin,numeric, zippable; 144 end:
IntToAscii := proc (i:posint) option builtin; 155 end:
AsciiToInt := proc (s:string) option builtin; 157 end:
size := proc(s) option builtin; 147 end:
Gamma := noeval( ReadLibrary(IncompleteGamma,Gamma)):
LnGamma := noeval( ReadLibrary(IncompleteGamma,LnGamma)):
Lngamma := noeval( ReadLibrary(IncompleteGamma,Lngamma)):

debug := proc( arg:string ) option builtin;  315 end:

assign := proc( a,v ) 
a := v; NULL end:

CodonToA := proc () 
  p := If (nargs = 3, CodonToInt(args[1], args[2], args[3]),
    CodonToInt(args[1]));
  If (p = 22, '$', IntToA(p))
end:

enum := proc(n:{integer,integer..integer})
  m := If (type (n, integer), 1..n, n);
  res := CreateArray (1..m[2]-m[1]+1);
  for i from m[1] to m[2] do res[i - m[1] + 1] := i od; res
end:

ReceiveDataTcp := noeval(ReadLibrary(IPC,ReceiveDataTcp)):
ReadTcp := noeval(ReadLibrary(IPC,ReadTcp)):
ReadData := noeval(ReadLibrary(ReadData,ReadData)):
Readability := noeval(ReadLibrary(Readability)):
SendDataTcp := noeval(ReadLibrary(IPC,SendDataTcp)):
GetAaCount := noeval(ReadLibrary(AaCount,GetAaCount)):
GetAaFrequency := noeval(ReadLibrary(AaFrequency)):
CalculateScore := noeval(ReadLibrary(CalculateScore)):
print := noeval(ReadLibrary(print)):
Document := noeval(ReadLibrary(Document)):
Table := noeval(ReadLibrary(Document,Table)):
Code := noeval(ReadLibrary(Document,Code)):
List := noeval(ReadLibrary(Document,List)):
printtext := noeval(ReadLibrary(DBTools,printtext)):
Paragraph := noeval(ReadLibrary(Document,Paragraph)):
TextBlock := noeval(ReadLibrary(Document, TextBlock)):
DocEl := noeval(ReadLibrary(Document, DocEl)):
Indent := noeval(ReadLibrary(Document,Indent)):
ConvertToEntityName := noeval(ReadLibrary(Document,ConvertToEntityName)):
convolve := noeval(ReadLibrary(convolve)):
GimpFigure := noeval(ReadLibrary(Document,GimpFigure)):
PostscriptFigure := noeval(ReadLibrary(Document,PostscriptFigure)):
PrintMatrix := noeval(ReadLibrary(print,PrintMatrix)):
Primes := noeval(ReadLibrary(Iterators)):
Indets := noeval(ReadLibrary(Iterators)):
Infix := noeval(ReadLibrary(Iterators)):
Prefix := noeval(ReadLibrary(Iterators)):
Postfix := noeval(ReadLibrary(Iterators)):
Leaves := noeval(ReadLibrary(Iterators)):
Lines := noeval(ReadLibrary(Iterators)):
Match_print := noeval(ReadLibrary(print,Match_print)):
CreateDayMatrices := noeval(ReadLibrary(CreateDayMatrices)):
DayMatrix := noeval(ReadLibrary(CreateDayMatrices,DayMatrix)):
Identity := noeval(ReadLibrary(Identity)):
SearchDb := noeval(ReadLibrary(SearchDF,SearchDb)):
SearchID := noeval(ReadLibrary(SearchDF,SearchID)):
SearchAC := noeval(ReadLibrary(SearchDF,SearchAC)):
GetEntryInfo := noeval(ReadLibrary(EntryInfo)):
PrintInfo := noeval(ReadLibrary(EntryInfo,PrintInfo)):
PatEntry := noeval(ReadLibrary(Entries,PatEntry)):
Entry := noeval(ReadLibrary(Entries,Entry)):
Entries := noeval(ReadLibrary(Entries)):
Sequence := noeval(ReadLibrary(Entries,Sequence)):
Sequences := noeval(ReadLibrary(Entries,Sequences)):
SequenceComplexity := noeval(ReadLibrary(SequenceComplexity)):
string := noeval(ReadLibrary(Entries,string)):
table := noeval(ReadLibrary(table)):
SplitLines := noeval(ReadLibrary(SplitLines)):
ID := noeval(ReadLibrary(Entries,ID)):
atoi := noeval(ReadLibrary(atoi)):
CreateRandPermutation := noeval(ReadLibrary(RandomPermut)):
Permutation := noeval(ReadLibrary(Permutation)):
Shuffle := noeval(ReadLibrary(RandomPermut,Shuffle)):
SetRandSeed := noeval(ReadLibrary(RandomPermut,SetRandSeed)):
Mutate := noeval(ReadLibrary(RandomPermut,Mutate)):
CreateRandSeq := noeval(ReadLibrary(RandomPermut,CreateRandSeq)):
Stat := noeval(ReadLibrary(Stat)):
Counter := noeval(ReadLibrary(Counter)):
StatTest := noeval(ReadLibrary(StatTest)):
TestGradHessian := noeval(ReadLibrary(TestGradHessian)):
Zscore := noeval(ReadLibrary(Zscore)):
ZscorePercent := noeval(ReadLibrary(Zscore,ZscorePercent)):
avg := noeval(ReadLibrary(Stat,avg)):
var := noeval(ReadLibrary(Stat,var)):
std := noeval(ReadLibrary(Stat,std)):
CollectStat := noeval(ReadLibrary(Stat,CollectStat)):
Polar := noeval(ReadLibrary(Polar)):
UpdateStat := noeval(ReadLibrary(Stat,UpdateStat)):
OutsideBounds := noeval(ReadLibrary(OutsideBounds)):
LinearRegression := noeval(ReadLibrary(Stat,LinearRegression)):
Covariance := noeval(ReadLibrary(Covariance)):
Cumulative := noeval(ReadLibrary(Cumulative)):
CumulativeStd := noeval(ReadLibrary(Cumulative,CumulativeStd)):
Std_Score := noeval(ReadLibrary(Cumulative,Std_Score)):
ExpFit := noeval(ReadLibrary(Stat,ExpFit)):
ExpFit2 := noeval(ReadLibrary(Stat,ExpFit2)):
MaxLikelihoodSize := noeval(ReadLibrary(Stat,MaxLikelihoodSize)):
ProbBallsBoxes := noeval(ReadLibrary(ProbBallsBoxes)):
lnProbBallsBoxes := noeval(ReadLibrary(ProbBallsBoxes,lnProbBallsBoxes)):
ProbCloseMatches := noeval(ReadLibrary(ProbBallsBoxes,ProbCloseMatches)):
PerIdentToPam := noeval(ReadLibrary(PItoPam)):
PamToPerIdent := noeval(ReadLibrary(PItoPam,PamToPerIdent)):
DrawGraph := noeval(ReadLibrary(Graph,DrawGraph)):
DrawHistogram := noeval(ReadLibrary(Histogram)):
DrawDistribution := noeval(ReadLibrary(Histogram,DrawDistribution)):
DrawDotplot := noeval(ReadLibrary(Histogram,DrawDotplot)):
DrawPointDistribution := noeval(ReadLibrary(Histogram,DrawPointDistribution)):
SmoothData := noeval(ReadLibrary(Histogram,SmoothData)):
DrawStackedBar := noeval(ReadLibrary(Histogram,DrawStackedBar)):
ViewPlot := noeval(ReadLibrary(Histogram,ViewPlot)):
Plot2Gif := noeval(ReadLibrary(Plot2Gif)):
View := noeval(ReadLibrary(View)):
SystemCommand := noeval(ReadLibrary(SystemCommand)):
StartOverlayPlot := noeval(ReadLibrary(Histogram,StartOverlayPlot)):
StopOverlayPlot := noeval(ReadLibrary(Histogram,StopOverlayPlot)):
GetColorMap := noeval(ReadLibrary(Histogram,GetColorMap)):
DrawTree := noeval(ReadLibrary(DrawPackage,DrawTree)):
string_RGB := noeval(ReadLibrary(Color,string_RGB)):
RGB_string := noeval(ReadLibrary(Color,RGB_string)):
ColorPalette := noeval(ReadLibrary(Color,ColorPalette)):
BrightenColor := noeval(ReadLibrary(Color,BrightenColor)):
CrossReference := noeval(ReadLibrary(CrossReference)):
ShortNames := noeval(ReadLibrary(CrossReference,ShortNames)):
CollapseNodes := noeval(ReadLibrary(SummarizeTree)):
PrintTreeSeq := noeval(ReadLibrary(SummarizeTree,PrintTreeSeq)):
SearchFrag := noeval(ReadLibrary(SearchFrag)):
GetMolWeight := noeval(ReadLibrary(MolWeight,GetMolWeight)):
NucPepMatch := noeval(ReadLibrary(NPMatch)):
NucPepMatch_print := noeval(ReadLibrary(NPMatch, NucPepMatch_print)):
LocalNucPepAlign := noeval(ReadLibrary(NPMatch,LocalNucPepAlign)):
GlobalNucPepAlign := noeval(ReadLibrary(NPMatch,GlobalNucPepAlign)):
LocalNucPepAlignBestPam := noeval(ReadLibrary(NPMatch,LocalNucPepAlignBestPam)):
GetPeptides := noeval(ReadLibrary(NPMatch,GetPeptides)):
GetIntrons := noeval(ReadLibrary(NPMatch,GetIntrons)):
AlignNucPepAll := noeval(ReadLibrary(NPMatch,AlignNucPepAll)):
VisualizeGene := noeval(ReadLibrary(NPMatch,VisualizeGene)):
NucID := noeval(ReadLibrary(NPMatch,NucID)):
MaximizeFunc := noeval(ReadLibrary(Maximize)):
MaximizeRD := noeval(ReadLibrary(Maximize)):
BestSearchString := noeval(ReadLibrary(BestStringMatch)):
PrintStringMatch := noeval(ReadLibrary(BestStringMatch,PrintStringMatch)):
Matrices := noeval(ReadLibrary(Matrices)):
FindEntropy := noeval(ReadLibrary(Matrices,FindEntropy)):
DayMatrixScale := noeval(ReadLibrary(Matrices,DayMatrixScale)):
ParExecuteIPC := noeval(ReadLibrary(ParExec2)):
GetMachineUsage := noeval(ReadLibrary(ParExec2,GetMachineUsage)):
ParExecuteTest := noeval(ReadLibrary(ParExec2,ParExecuteTest)):
ParExecSlave := noeval(ReadLibrary(ParExecSlave)):
MinimizeFunc := noeval(ReadLibrary(Minimize)):
DisconMinimize := noeval(ReadLibrary(Minimize,DisconMinimize)):
BFGSMinimize := noeval(ReadLibrary(BFGSMinimize,BFGSMinimize)):
Minimize2DFunc := noeval(ReadLibrary(Minimize,Minimize2DFunc)):
MinimizePWC := noeval(ReadLibrary(Minimize,MinimizePWC)):
MinimizeSD := noeval(ReadLibrary(Minimize,MinimizeSD)):
MinimizeBrent := noeval(ReadLibrary(Minimize,MinimizeBrent)):
DbToDarwin := noeval(ReadLibrary(ConvertToDF)):
SpToDarwin := noeval(ReadLibrary(ConvertSP)):
sign := noeval(ReadLibrary(sign)):
Zeta := noeval(ReadLibrary(Zeta)):
Graph := noeval(ReadLibrary(Graph)):
TetrahedronGraph := noeval(ReadLibrary(Graph,TetrahedronGraph)):
HexahedronGraph := noeval(ReadLibrary(Graph,HexahedronGraph)):
CubeGraph := noeval(ReadLibrary(Graph,CubeGraph)):
OctahedronGraph := noeval(ReadLibrary(Graph,OctahedronGraph)):
IcosahedronGraph := noeval(ReadLibrary(Graph,IcosahedronGraph)):
DodecahedronGraph := noeval(ReadLibrary(Graph,DodecahedronGraph)):
PetersenGraph := noeval(ReadLibrary(Graph,PetersenGraph)):
BipartiteGraph := noeval(ReadLibrary(Graph,BipartiteGraph)):
BipartiteMatching := noeval(ReadLibrary(BipartiteMatching)):
Complete := noeval(ReadLibrary(Graph,Complete)):
RegularGraph := noeval(ReadLibrary(Graph,RegularGraph)):
Edge := noeval(ReadLibrary(Graph,Edge)):
EdgeComplement := noeval(ReadLibrary(Graph,EdgeComplement)):
ShortestPath := noeval(ReadLibrary(Graph,ShortestPath)):
InduceGraph := noeval(ReadLibrary(Graph,InduceGraph)):
FindConnectedComponents := noeval(ReadLibrary(Graph,FindConnectedComponents)):
ParseDimacsGraph := noeval(ReadLibrary(Graph, ParseDimacsGraph)):
Tree := noeval(ReadLibrary(Tree)):
TreeResult := noeval(ReadLibrary(TreeResult)):
RellTree := noeval(ReadLibrary(TreeResult)):
AllAllResult := noeval(ReadLibrary(TreeResult,AllAllResult)):
AlSumm := noeval(ReadLibrary(TreeResult,AlSumm)):
GetTreeLabels := noeval(ReadLibrary(Tree,GetTreeLabels)):
DigestSeq := noeval(ReadLibrary(MassProfile,DigestSeq)):
DigestWeights := noeval(ReadLibrary(MassProfile,DigestWeights)):
Gene := noeval(ReadLibrary(Gene)):
GetComplement := noeval(ReadLibrary(Gene,GetComplement)):
ComplementSequence := noeval(ReadLibrary(Gene,ComplementSequence)):
Complement := noeval(ReadLibrary(Gene,Complement)):
Reverse := noeval(ReadLibrary(Gene,Reverse)):
help := noeval(ReadLibrary(help)):
IntronModel := noeval(ReadLibrary(IntronScores,IntronModel)):
LinearIntron := noeval(ReadLibrary(IntronScores,LinearIntron)):
Intron := noeval(ReadLibrary(IntronScores,Intron)):
Fold := noeval(ReadLibrary(Fold)):
ReadBrk := noeval(ReadLibrary(Fold,ReadBrk)):
ReadDssp := noeval(ReadLibrary(Fold,ReadDssp)):
CreateCProgram := noeval(ReadLibrary(ExtCallFrame)):
PredictGenes := noeval(ReadLibrary(PredictGenes)):
PamWindows := noeval(ReadLibrary(StructurePrediction,PamWindows)):
SurfIntActPred := noeval(ReadLibrary(StructurePrediction,SurfIntActPred)):
ParsePred := noeval(ReadLibrary(StructurePrediction,ParsePred)):
PrintPV := noeval(ReadLibrary(ProbModel,PrintPV)):
MostProbAA := noeval(ReadLibrary(ProbModel,MostProbAA)):
ProbTree := noeval(ReadLibrary(ProbModel,ProbTree)):
ConvertTree := noeval(ReadLibrary(ProbModel,ConvertTree)):

# Added 05.02.97, Chantal Korostensky
WriteFasta := noeval(ReadLibrary(FileConv, WriteFasta)):
ReadMap    := noeval(ReadLibrary(FileConv, ReadMap)):
ReadFasta  := noeval(ReadLibrary(FileConv, ReadFasta)):
ReadPir    := noeval(ReadLibrary(FileConv, ReadPir)):
ReadPima   := noeval(ReadLibrary(FileConv, ReadPima)):
ReadMsa  := noeval(ReadLibrary(FileConv, ReadMsa)):
IdenticalTrees   := noeval(ReadLibrary(TreeUtil, IdenticalTrees)):
GetMATreeNew   := noeval(ReadLibrary(TreeUtil, GetMATreeNew)):
UnlabelLeaves   := noeval(ReadLibrary(TreeUtil, UnlabelLeaves)):
AddSpecies := noeval(ReadLibrary(TreeUtil, AddSpecies)):
FindRules  := noeval(ReadLibrary(TreeUtil, FindRules)):
FindSpeciesViolations := noeval(ReadLibrary(TreeUtil, FindSpeciesViolations)):
GetPathDistance    := noeval(ReadLibrary(TreeUtil, GetPathDistance)):
TotalTreeWeight    := noeval(ReadLibrary(TreeUtil, TotalTreeWeight)):
FindCircularOrder  := noeval(ReadLibrary(Tree, FindCircularOrder)):
CircularTour := noeval(ReadLibrary(CircularTour)):
Clusters := noeval(ReadLibrary(CircularTour,Clusters)):
Species_Entry  := noeval(ReadLibrary(Species,Species_Entry)):
SP_Species  := noeval(ReadLibrary(Species,SP_Species)):
SPCommonName  := noeval(ReadLibrary(Species,SPCommonName)):
Orthologues  := noeval(ReadLibrary(Orthologues)):
PhylogeneticTree  := noeval(ReadLibrary(PhylogeneticTree)):
GapTree  := noeval(ReadLibrary(GapTree)):
OptimizeTree  := noeval(ReadLibrary(PhylogeneticTree,OptimizeTree)):
RBFS_Tree  := noeval(ReadLibrary(RBFS_tree)):
ComputeDimensionlessFit := noeval(ReadLibrary(RBFS_tree,ComputeDimensionlessFit)):
RemoveUnchanged  := noeval(ReadLibrary(PhylogeneticTree,RemoveUnchanged)):
Synteny  := noeval(ReadLibrary(Synteny)):
SignedSynteny  := noeval(ReadLibrary(SignedSynteny)):
dSplits  := noeval(ReadLibrary(dSplits)):
KWIndex  := noeval(ReadLibrary(VariationIndices,KWIndex)):
ProbIndex  := noeval(ReadLibrary(VariationIndices,ProbIndex)):
ScaleIndex  := noeval(ReadLibrary(VariationIndices,ScaleIndex)):
PrintIndex  := noeval(ReadLibrary(VariationIndices,PrintIndex)):
PlotIndex  := noeval(ReadLibrary(VariationIndices,PlotIndex)):
ParseNewickTree := noeval(ReadLibrary(Newick2Darwin, ParseNewickTree)):
BinaryNewick2Darwin := noeval(ReadLibrary(Newick2Darwin, BinaryNewick2Darwin)):

# Added 10.02.97, Chantal Korostensky
HTMLC  := noeval(ReadLibrary(HTMLCTools, HTMLC)):
HTML  := noeval(ReadLibrary(HTMLCTools, HTML)):
HyperLink  := noeval(ReadLibrary(HTMLCTools, HyperLink)):
PlusMin  := noeval(ReadLibrary(HTMLCTools, PlusMin)):
HTMLColor  := noeval(ReadLibrary(HTMLTools, HTMLColor)):
Center := noeval(ReadLibrary(HTMLCTools,Center)):
WeightObservations := noeval(ReadLibrary(WeightObservations)):
SVD := noeval(ReadLibrary(SVD)):
SvdResult := noeval(ReadLibrary(SvdAnalysis,SvdResult)):
SvdAnalysis := noeval(ReadLibrary(SvdAnalysis)):
SvdBestBasis := noeval(ReadLibrary(SvdBestBasis)):
LinearClassify := noeval(ReadLibrary(LinearClassify)):
LinearClassification := noeval(ReadLibrary(LinearClassify,LinearClassification)):
LinearProgramming := noeval(ReadLibrary(LinearProgramming)):
CreateDB := noeval(ReadLibrary(DBTools, CreateDB)):
Description := noeval(ReadLibrary(Description)):
HelpEntry := noeval(ReadLibrary(Description,HelpEntry)):
Descriptions := noeval(ReadLibrary(Descriptions)):
mselect := noeval(ReadLibrary(AlgManipulation,mselect)):
hastype := noeval(ReadLibrary(AlgManipulation,hastype)):
indets := noeval(ReadLibrary(AlgManipulation,indets)):
algebraic_type := noeval(ReadLibrary(AlgManipulation,algebraic_type)):
subs := noeval(ReadLibrary(AlgManipulation,subs)):
coeff := noeval(ReadLibrary(AlgManipulation,coeff)):
lcoeff := noeval(ReadLibrary(AlgManipulation,lcoeff)):
gcd := noeval(ReadLibrary(AlgManipulation,gcd)):
PartialFraction := noeval(ReadLibrary(AlgManipulation,PartialFraction)):
LongInteger := noeval(ReadLibrary(LongInteger)):
Complex := noeval(ReadLibrary(Complex)):
Inherit := noeval(ReadLibrary(Inherit)):
ExtendClass := noeval(ReadLibrary(Inherit,ExtendClass)):
Protect := noeval(ReadLibrary(Inherit,Protect)):
GetMethods := noeval(ReadLibrary(Inherit,GetMethods)):
CompleteClass := noeval(ReadLibrary(Inherit,CompleteClass)):
Introspection := noeval(ReadLibrary(Inherit,Introspection)):
list_power := noeval(ReadLibrary(list_power)):
set_power := noeval(ReadLibrary(set_power)):
GramSchmidt := noeval(ReadLibrary(GramSchmidt)):
GivensElim := noeval(ReadLibrary(GivensElim)):
gigahertz := noeval(ReadLibrary(gigahertz)):
LSBestSum := noeval(ReadLibrary(LSBestSum)):
LSBestDelete := noeval(ReadLibrary(LSBestSum,LSBestDelete)):
LSBestSumDelete := noeval(ReadLibrary(LSBestSum,LSBestSumDelete)):
ContinuedFraction := noeval(ReadLibrary(ContinuedFraction)):

# *** ADDED FROM CH.K, 3.8.98 ***
MSAMethod := noeval(ReadLibrary(MSAParameters, MSAMethod)):
MSAStatistics := noeval(ReadLibrary(MSAParameters, MSAStatistics)):
MSA_CT := noeval(ReadLibrary(MSA_CT)):
Gap := noeval(ReadLibrary(GapH, Gap)):
GapHeuristic := noeval(ReadLibrary(GapH, GapHeuristic)):
DoGapHeuristic := noeval(ReadLibrary(GapH, DoGapHeuristic)):
TreeConstruction := noeval(ReadLibrary(TreeParameters, TreeConstruction)):
rawprint := noeval(ReadLibrary(TreeParameters, rawprint)):
TreeStatistics := noeval(ReadLibrary(TreeParameters, TreeStatistics)):
Partitions := noeval(ReadLibrary(Partitions, Partitions)):
ResolveConflicts := noeval(ReadLibrary(Partitions, ResolveConflicts)):
GetConflicts := noeval(ReadLibrary(Partitions, GetConflicts)):
GetTree := noeval(ReadLibrary(Tree, GetTree)):
ChangeLeafLabels := noeval(ReadLibrary(Tree, ChangeLeafLabels)):
GetPartitions := noeval(ReadLibrary(Partitions, GetPartitions)):
#CreateRandMultAlign := noeval(ReadLibrary(RandomMSA, CreateRandMultAlign)):
CreateRandMultAlign := noeval(ReadLibrary(RandomMSA)):
LLL := noeval(ReadLibrary(LLL)):
GapMatch := noeval(ReadLibrary(DynProgGap, GapMatch)):
DynProgGap := noeval(ReadLibrary(DynProgGap, DynProgGap)):
Roman := noeval(ReadLibrary(Roman)):
Alphabetical := noeval(ReadLibrary(Roman,Alphabetical)):
Alphanumerical := noeval(ReadLibrary(Roman,Alphanumerical)):
Ordinal := noeval(ReadLibrary(Roman,Ordinal)):
# ***

Parsimony_merge_e := proc( x, y ) option builtin, internal; 241 end:
Parsimony_cost_e := proc( x, y ) option builtin, internal; 242 end:
compress := proc( x ) option builtin; 243 end:
decompress := proc( x ) option builtin; 244 end:
DynProgRowSpecial := proc( rf:array(list,2),
	rf1:array(list,2), iSeq2:list, sco:list, C0:numeric,
	C1:numeric, minscore:numeric ) option builtin; 245 end:
ServerSocket_internal := proc( socket_path:string ) option builtin, internal; 246 end:
ServerSocket := proc( socket_path:string; (gcf=10^10):posint ) 
   Set(quiet=true); 
   Set(batch=true);
   Set(gc=gcf);
   ServerSocket_internal( args );
end:

exit := proc(e:{0,posint}) option builtin; 247 end:

FileStat := noeval(ReadLibrary(FileStat)):
NormalizePath := noeval(ReadLibrary(FileStat, NormalizePath)):

LinearClassify_X0 := proc( AX:list(numeric), wneg:numeric,
	wpos:numeric, sb:posint, b:list, ind0:name )
	option builtin; 259 end:
DynProgScore := proc( seq1:{string,structure}, seq2:{string,structure},
	dm:DayMatrix, modif:{string,structure,set({string,structure})} )
	option builtin; 260 end:
DynProgBoth := proc( seq1:string, seq2:string,
	dm:DayMatrix, modif:{string,structure,set({string,structure})} )
	option builtin; 269 end:
TPIDistr := proc( m1:{0,posint}, m2:{0,posint}, m3:{0,posint}, m4:{0,posint} )
	option builtin; 261 end:
LinearClassification_DirOpt2 := proc( AX:list, Adx:list, wneg:numeric,
	wpos:numeric, sb:posint, b:list(integer) ) option builtin; 262 end: 
LinearClassification_DirOpt3 := proc( AX:list, Adx:list, wneg:numeric,
	wpos:numeric, sb:posint, b:list(integer) ) option builtin; 263 end: 
LinearClassification_DirOpt4 := proc( AX:list, Adx:list, wneg:numeric,
	wpos:numeric, sb:posint, b:list(integer) ) option builtin; 264 end: 
ComputeTPI := noeval(ReadLibrary(ComputeTPI)):

TotalAlign := proc( m:Match, DM:DayMatrix, goal:numeric ) option builtin;
178 end:


#from florida Marcel Turcotte
ExpandFileName := noeval(ReadLibrary(MBA_Toolkit, ExpandFileName)):
ReadFastaWithNames := noeval(ReadLibrary(MBA_Toolkit, ReadFastaWithNames)):
WriteDarwinDb := noeval(ReadLibrary(MBA_Toolkit,WriteDarwinDb)):
FastaToDarwinDb := noeval(ReadLibrary(MBA_Toolkit,FastaToDarwinDb)):

# Stefan Zoller, Aug 2011
ReadPhylip := noeval(ReadLibrary(MBA_Toolkit, ReadPhylip)):
#codon stuff gmc Aug 2, 2001

AToCodon := noeval(ReadLibrary(CodonTools, AToCodon)):
IntToCodon := noeval(ReadLibrary(CodonTools, IntToCodon)):
#CodonToInt := noeval(ReadLibrary(CodonTools, CodonToInt)):
CIntToInt := noeval(ReadLibrary(CodonTools, CIntToInt)):
CIntToA := noeval(ReadLibrary(CodonTools, CIntToA)):
CodonToAAA := noeval(ReadLibrary(CodonTools, CodonToAAA)):
CIntToAAA := noeval(ReadLibrary(CodonTools, CIntToAAA)):
CodonToAmino := noeval(ReadLibrary(CodonTools, CodonToAmino)):
CIntToAmino := noeval(ReadLibrary(CodonTools, CIntToAmino)):
AltGenCode := noeval(ReadLibrary(CodonTools, AltGenCode)):
CodonToCInt := noeval(ReadLibrary(CodonTools, CodonToCInt)):
SetuptRNA := noeval(ReadLibrary(SetuptRNA)):
NucToCode := noeval(ReadLibrary(CodonTools,NucToCode)):
CodeToNuc := noeval(ReadLibrary(CodonTools,CodeToNuc)):
CIntToCodon := noeval(ReadLibrary(CodonTools,CIntToCodon)):
AToCInt := noeval(ReadLibrary(CodonTools,AToCInt)):
IntToCInt := noeval(ReadLibrary(CodonTools,IntToCInt)):

#dna stuff gmc Aug 5, 2002
CheckDNA := noeval(ReadLibrary(DNATools, CheckDNA)):
CreateDNAAlignFromProtein := noeval(ReadLibrary(DNATools, CreateDNAAlignFromProtein)):
CreateUngappedSequence := noeval(ReadLibrary(DNATools, CreateUngappedSequence)):
CreateProteinAlignFromDNA := noeval(ReadLibrary(DNATools, CreateProteinAlignFromDNA)):
ConsistentGenome := noeval(ReadLibrary(ConsistentGenome)):
GenomeSummary := noeval(ReadLibrary(GenomeSummary)):

#counting bases, SearchAllArray, PvR, Feb 20, 2003
BaseCount := noeval(ReadLibrary(CodonCountsLib,BaseCount)):
SearchAllArray := noeval(ReadLibrary(SearchAllArray)):
#
# Number of accepted point mutations, from:
#  A Model of Evolutionary Change in Proteins by
#  M.O. Dayhoff, R.M. Schwartz and B.C. Orcutt.
Mutations1978 := [
  [  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 0, 0, 0, 0],
  [ 30,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 0, 0, 0, 0],
  [109, 17,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 0, 0, 0, 0],
  [154,  0,532,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 0, 0, 0, 0],
  [ 33, 10,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 0, 0, 0, 0],
  [ 93,120, 50, 76,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 0, 0, 0, 0],
  [266,  0, 94,831,  0,422,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 0, 0, 0, 0],
  [579, 10,156,162, 10, 30,112,  0,  0,  0,  0,  0,  0,  0,  0,  0, 0, 0, 0, 0],
  [ 21,103,226, 43, 10,243, 23, 10,  0,  0,  0,  0,  0,  0,  0,  0, 0, 0, 0, 0],
  [ 66, 30, 36, 13, 17,  8, 35,  0,  3,  0,  0,  0,  0,  0,  0,  0, 0, 0, 0, 0],
  [ 95, 17, 37,  0,  0, 75, 15, 17, 40,253,  0,  0,  0,  0,  0,  0, 0, 0, 0, 0],
  [ 57,477,322, 85,  0,147,104, 60, 23, 43, 39,  0,  0,  0,  0,  0, 0, 0, 0, 0],
  [ 29, 17,  0,  0,  0, 20,  7,  7,  0, 57,207, 90,  0,  0,  0,  0, 0, 0, 0, 0],
  [ 20,  7,  7,  0,  0,  0,  0, 17, 20, 90,167,  0, 17,  0,  0,  0, 0, 0, 0, 0],
  [345, 67, 27, 10, 10, 93, 40, 49, 50,  7, 43, 43,  4,  7,  0,  0, 0, 0, 0, 0],
  [772,137,432, 98,117, 47, 86,450, 26, 20, 32,168, 20, 40,269,  0, 0, 0, 0, 0],
  [590, 20,169, 57, 10, 37, 31, 50, 14,129, 52,200, 28, 10, 73,696, 0, 0, 0, 0],
  [  0, 27,  3,  0,  0,  0,  0,  0,  3,  0, 13,  0,  0, 10,  0, 17, 0, 0, 0, 0],
  [ 20,  3, 36,  0, 30,  0, 10,  0, 40, 13, 23, 10,  0,260,  0, 22,23, 6, 0, 0],
  [365, 20, 13, 17, 33, 27, 37, 97, 30,661,303, 17, 77, 10, 50, 43,186,0,17,0]]:
DBL_EPSILON := 2.2204460492503131*10^(-16):
DBL_MAX := 1.7976931348623147*10^308:
Pi := -0.32584135910528735661672e-06 + 3294199/1048576:
# Matrix generated on Mon Nov  4 05:29:35 MET 1991
# from sample with PAM from 6.4 to 100.0 extrapolated to 116.5
# random vs random gives -0.62196 similarity
NewLogPAM1 := [[ -94849167.5024, 4544331.5392, 3950895.7642, 5075559.2685,
    10509486.6552, 7821215.6793, 9284867.4577, 10208268.6773,
    4128730.4460, 2088402.6725, 3942030.3556, 5544102.9591,
    7873192.1288, 2081786.9806, 8933017.3353, 25463979.0926,
    12087687.9616, 938717.6754, 1816599.3219, 14779792.0604],
   [ 3088606.9019, -79929382.8416, 4269239.6312, 1655233.1266,
    1736199.9907, 13919517.8286, 3630902.6919, 2602718.2624,
    6947846.1049, 926558.7304, 1807263.7386, 25753650.3430,
    1710966.8045, 350093.8734, 2237195.6388, 4166759.1691,
    3978330.3745, 3253232.5391, 2289634.0815, 1544649.7457],
   [ 2290927.3283, 3642282.6431, -96451119.9812, 15734455.2696,
    1516899.1156, 7178694.2982, 4353788.4775, 4771506.9422,
    11545580.2546, 1102105.6247, 656762.2820, 8464648.9678,
    1137719.5856, 878876.5516, 1538902.9216, 11023119.2471,
    6900696.3646, 570925.9280, 2766153.3106, 743887.8388],
   [ 3470266.3186, 1665119.6347, 18553031.1074, -81923956.4087,
    276028.4793, 6226313.0607, 24312537.5194, 4134242.6743,
    5282013.4703, 188341.4823, 131158.4714, 4149263.8609,
    236419.6850, 223657.2420, 2479252.1442, 6226729.7105,
    4557332.3643, 77176.2019, 1205027.7108, 179487.3608],
   [ 2522064.2915, 613030.0599, 627791.7545, 96883.4602,
    -46823529.9064, 216095.4307, 43613.4399, 489113.7805,
    995254.8196, 447266.9547, 570876.9633, 71989.8710,
    1127983.9013, 1033868.3428, 73686.9290, 2295153.6442,
    1121976.9695, 928124.3635, 1279520.8909, 1884650.4311],
   [ 3754699.1282, 9831786.5667, 5943340.3069, 4371725.9675,
    432286.6396, -124298615.8968, 15604785.8586, 1690312.4338,
    12104211.9812, 843586.2680, 2606859.1297, 12493678.3810,
    5420375.2816, 755560.3559, 3509155.2648, 4707458.9403,
    4148983.1610, 1264258.7211, 1249105.6978, 1313424.8190],
   [ 6901386.7806, 3970842.3038, 5581002.8430, 26430905.7693,
    135084.7585, 24161149.5137, -95466922.2113, 2105215.6424,
    5809977.3792, 952630.9241, 906956.1549, 12697999.5654,
    2157145.3021, 276111.1317, 3465447.4123, 5784171.0817,
    4183806.0648, 556528.0589, 958942.6584, 2712747.7789],
   [ 9555577.7381, 3584589.1700, 7702730.0356, 5660071.5590,
    1907831.9028, 3295876.7633, 2651189.5986, -41190659.0280,
    2465528.1371, 211987.5938, 491124.0624, 2569041.9933,
    1091377.8601, 377442.8186, 2051441.8768, 8478517.4003,
    1831897.2059, 1404167.8359, 688481.4858, 704639.7340],
   [ 1236548.8172, 3061627.1303, 5963411.2455, 2313744.1798,
    1242093.7478, 7551450.4635, 2341038.2998, 788859.8300,
    -90660120.4886, 588718.8936, 732377.8326, 2803016.8479,
    1554270.9098, 1775938.6189, 1066164.1001, 1921603.5205,
    2153123.2181, 1046731.2440, 7786680.5888, 447060.1420],
   [ 1543249.4441, 1007400.6166, 1404524.6535, 203558.3731,
    1377254.0280, 1298525.5848, 947078.3419, 167350.6781,
    1452563.4971, -105165666.0254, 18851556.4458, 1878072.3685,
    22933389.7197, 5722207.3179, 885057.0022, 1172267.0207,
    4582762.4974, 1465194.3072, 2107443.0141, 36788470.9311],
   [ 4735652.4519, 3194396.0762, 1360668.4663, 230450.3133,
    2857772.9813, 6523438.0370, 1465836.3636, 630298.4116,
    2937651.7630, 30646803.3616, -70057672.5190, 2984548.3113,
    41990207.1426, 19031758.3366, 3378475.8298, 2163507.1296,
    3252921.6763, 4222106.5048, 4605829.1937, 16061545.5607],
   [ 4152442.7343, 28380401.2191, 10933660.2953, 4545320.5538,
    224682.4288, 19492242.5698, 12795198.0861, 2055600.4789,
    7009763.0300, 1903543.4708, 1860763.2506, -100965731.1416,
    4352426.8576, 470289.9972, 3370756.0739, 5565187.5825,
    7473159.9932, 435422.0564, 1721791.4731, 1965467.6037],
   [ 2286382.4161, 731049.8231, 569793.5322, 100415.9623,
    1364979.9529, 3278887.3660, 842784.9318, 338585.4592,
    1507058.1294, 9012481.4582, 10150470.6780, 1687551.9006,
    -122250535.0004, 4432083.6764, 149239.9440, 1329648.9217,
    2331130.0096, 1018524.1197, 1055358.4070, 3460802.9081],
   [ 1080457.2558, 267339.5323, 786653.4267, 169775.6359,
    2235948.9789, 816844.8685, 192794.4640, 209275.1254,
    3077545.7446, 4018953.6882, 8222243.9644, 325885.2310,
    7921022.2187, -66575606.6139, 385382.2694, 546638.3440,
    1161001.0985, 9013061.4954, 23971713.5077, 2358959.7055],
   [ 5187462.7012, 1911472.9004, 1541176.1992, 2105710.2259,
    178308.7342, 4244812.5339, 2707418.9482, 1272656.4091,
    2067217.2896, 695514.4604, 1633118.7637, 2613435.4097,
    298430.9531, 431198.4966, -49432932.9748, 5421906.4901,
    4429139.5737, 241454.6074, 844692.9784, 1353701.1962],
   [ 19589024.4498, 4716201.0426, 14624307.2847, 7005959.9761,
    7357387.8850, 7543487.9401, 5986417.6133, 6967894.9909,
    4935777.6656, 1220369.0856, 1385431.3541, 5716023.1857,
    3522293.1905, 810243.0773, 7182601.1733, -119150506.2689,
    27955884.4072, 1515129.0644, 3323057.5421, 1912272.3447],
   [ 9500142.4571, 4600394.6942, 9353282.5694, 5238641.4917,
    3674482.3830, 6792469.0774, 4423823.2151, 1538094.8555,
    5650163.6266, 4874076.4730, 2128142.1131, 7841854.7268,
    6308924.7995, 1758118.7508, 5994451.2590, 28561010.8460,
    -104950600.4902, 717314.3721, 1760999.6535, 10434752.8601],
   [ 156259.3029, 796770.7189, 163898.4750, 18789.5071,
    643787.3073, 438375.1885, 124634.2181, 249703.7416,
    581770.0213, 330053.4075, 585032.7973, 96771.8284,
    583827.0101, 2890759.2177, 69213.3028, 327849.0859,
    151926.5032, -38106197.0662, 3439097.9644, 154814.9186],
   [ 757720.7584, 1405152.5941, 1989805.1163, 735136.8110,
    2223938.4753, 1085296.3624, 538123.5728, 306787.3482,
    10844453.2596, 1189553.5260, 1599182.4235, 958866.6753,
    1515835.2069, 19265390.3976, 606725.3087, 1801778.3322,
    934592.7996, 8617547.7310, -65919093.5252, 1441395.6510],
   [ 13040296.2262, 2005194.5764, 1131907.2743, 231618.9579,
    6929075.4620, 2413923.3304, 3220089.1130, 664173.2866,
    1317013.8687, 43924717.9500, 11796321.7380, 2315328.7151,
    10514726.4429, 4010221.4303, 2056767.1888, 2193220.7099,
    11714248.2474, 820580.2399, 3048964.0446, -100242523.5904]
    ] / (2048*2048*2048):
logPAM1 := NewLogPAM1:

# Human mitochondrial DNA count matrix (based on very short PAM evolution)
#  taken from 86 full mtDNA genomes (also used for Eve's tree)
HumanMtDNA := [
[438851,0,0,0,74,0,0,997,0,0,0,0,0,0,0,0,56.5,0,0,0],
[0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
[0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
[0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
[74,0,0,0,444246,0,0,16.5,0,0,0,0,0,0,0,0,1199,0,0,0],
[0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0],
[997,0,0,0,16.5,0,0,186126,0,0,0,0,0,0,0,0,4,0,0,0],
[0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0],
[56.5,0,0,0,1199,0,0,4,0,0,0,0,0,0,0,0,350736,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1]]:

# RNA viruses.  Count matrix taken from 50 RNA viruses
ViralRNA := [
[72271,0,0,0,10471,0,0,14868.5,0,0,0,0,0,0,0,0,11546.5,0,0,0],
[0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
[0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
[0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
[10471,0,0,0,45021,0,0,6789,0,0,0,0,0,0,0,0,13742,0,0,0],
[0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0],
[14868.5,0,0,0,6789,0,0,57924,0,0,0,0,0,0,0,0,7237.5,0,0,0],
[0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0],
[11546.5,0,0,0,13742,0,0,7237.5,0,0,0,0,0,0,0,0,73792,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1]]:

BacterialtRNA:=[
[4641,0,0,0,139.5,0,0,1247.5,0,0,0,0,0,0,0,0,187.5,0,0,0],
[0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
[0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
[0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
[139.5,0,0,0,6175,0,0,157.5,0,0,0,0,0,0,0,0,911.5,0,0,0],
[0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0],
[1247.5,0,0,0,157.5,0,0,8287,0,0,0,0,0,0,0,0,151.5,0,0,0],
[0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0],
[187.5,0,0,0,911.5,0,0,151.5,0,0,0,0,0,0,0,0,5700,0,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1]]:


latex := noeval(ReadLibrary(LaTeXCTools, latex)):
LaTeX := noeval(ReadLibrary(LaTeXCTools, LaTeX)):
LaTeXC := noeval(ReadLibrary(LaTeXCTools, LaTeXC)):
MAlign := noeval(ReadLibrary(MSA, MAlign)):
MAlignment := noeval(ReadLibrary(MSA, MAlignment)):

PartialOrder := noeval(ReadLibrary(PartialOrder)):
PartialOrderMSA := noeval(ReadLibrary(PartialOrder, PartialOrderMSA)):
PartialOrderMSA_MAlign := noeval(ReadLibrary(PartialOrder, PartialOrderMSA_MAlign)):
SeqThread := noeval(ReadLibrary(PartialOrder, SeqThread)):
DynProgBoth_PartOrd_G := noeval(ReadLibrary(DynProgBoth_PartOrd)):
DynProgBoth_PartOrd_D := noeval(ReadLibrary(DynProgBoth_PartOrd_D)):

# Codon Transition Matrices
# Adrian Schneider, 2004
# edited April 2005 and August 2006
CreateCodonMatrices := noeval(ReadLibrary(CodonMatrix,CreateCodonMatrices)):
CreateSynMatrices := noeval(ReadLibrary(CodonMatrix,CreateSynMatrices)):
CodonPamToPam := noeval(ReadLibrary(CodonMatrix,CodonPamToPam)):
PamToCodonPam := noeval(ReadLibrary(CodonMatrix,PamToCodonPam)):
CodonAlign := noeval(ReadLibrary(CodonAlign,CodonAlign)):
CodonDynProgStrings := noeval(ReadLibrary(CodonAlign,CodonDynProgStrings)):
PrintCodonAlignment := noeval(ReadLibrary(CodonAlign,PrintCodonAlignment)):
CodonMutate := noeval(ReadLibrary(CodonMutate,CodonMutate)):
ScoreAlignment := noeval(ReadLibrary(CodonScore,ScoreAlignment)):
EstimateSynPAM := noeval(ReadLibrary(CodonScore,EstimateSynPAM)):
EstimateCodonPAM := noeval(ReadLibrary(CodonScore,EstimateCodonPAM)):
EstimateNG86 := noeval(ReadLibrary(NeiGojobori,EstimateNG86)):
EstimatePB93 := noeval(ReadLibrary(PamiloBianchi,EstimatePB93)):

# Boostrapping trees, added by AS
BootstrapTree := noeval(ReadLibrary(BootstrapTree,BootstrapTree)):
ShowBootstrap := noeval(ReadLibrary(BootstrapTree,ShowBootstrap)):

# Gene Ontologies, added by AS, Sept 2005
GOdownload := noeval(ReadLibrary(Ontology,GOdownload)):
GOdefinition := noeval(ReadLibrary(Ontology,GOdefinition)):
GOname := noeval(ReadLibrary(Ontology,GOname)):
GOsubclass := noeval(ReadLibrary(Ontology,GOsubclass)):
GOsubclassR := noeval(ReadLibrary(Ontology,GOsubclassR)):
GOsuperclassR := noeval(ReadLibrary(Ontology,GOsuperclassR)):
GOsuperclass := noeval(ReadLibrary(Ontology,GOsuperclass)):
GOnumber := noeval(ReadLibrary(Ontology,GOnumber)):

# Rotate Trees, added by CD, Oct 2005
RotateTree := noeval(ReadLibrary(RotateTree,RotateTree)):
AllRootedTrees := noeval(ReadLibrary(RotateTree,AllRootedTrees)):
AllTernaryRoots := noeval(ReadLibrary(RotateTree,AllTernaryRoots)):

# SearchAllString, added by AR, Nov 2005
SearchAllString := noeval(ReadLibrary(SearchAllString,SearchAllString)):
HammingSearchAllString := noeval(ReadLibrary(SearchAllString,HammingSearchAllString)):

# DNA <-> Protein tools, added by AR, Nov 2005
CodonCount := noeval(ReadLibrary(Translate,CodonCount)):
CodonUsage := noeval(ReadLibrary(Translate,CodonUsage)):
Translate := noeval(ReadLibrary(Translate,Translate)):
BackTranslate := noeval(ReadLibrary(Translate,BackTranslate)):
ReplaceString := noeval(ReadLibrary(Translate,ReplaceString)):
Transcribe := noeval(ReadLibrary(Translate,Transcribe)):
BackTranscribe := noeval(ReadLibrary(Translate,BackTranscribe)):

# Codon Bias Tools. Added by AR (Dec 2005 - April 2007)
RSCU := noeval(ReadLibrary(CodonIndices,RSCU)):
ComputeCAI := noeval(ReadLibrary(CodonIndices,ComputeCAI)):
ComputeCAIVector := noeval(ReadLibrary(CodonIndices,ComputeCAIVector)):
SetupRA := noeval(ReadLibrary(CodonIndices,SetupRA)):
ComputeCarboneRA := noeval(ReadLibrary(CodonIndices,ComputeCarboneRA)):
RelativeAdaptiveness := noeval(ReadLibrary(CodonIndices,RelativeAdaptiveness)):
FindHighlyExpressedGenes := noeval(ReadLibrary(CodonIndices,FindHighlyExpressedGenes)):
ComputeFop := noeval(ReadLibrary(CodonIndices,ComputeFop)):
ComputeNEC := noeval(ReadLibrary(CodonIndices,ComputeNEC)):
NucleotideContent := noeval(ReadLibrary(CodonIndices,NucleotideContent)):
ComputeGC3syn := noeval(ReadLibrary(CodonIndices,ComputeGC3syn)):


# Ancestor package, addded by AS, Dec 22, 2005
ProbSeq := noeval(ReadLibrary(Ancestor,ProbSeq)):
ProbAncestor := noeval(ReadLibrary(Ancestor,ProbAncestor)):
PASfromMSA := noeval(ReadLibrary(Ancestor,PASfromMSA)):
PASfromTree := noeval(ReadLibrary(Ancestor,PASfromTree)):
PSDynProg := noeval(ReadLibrary(Ancestor,PSDynProg)):

# Added by AR (Jan 2006)
WriteData := noeval(ReadLibrary(ReadData,WriteData)):

# Global variable functions by AS, Feb 2006
Globals := noeval(ReadLibrary(Globals,Globals)):
UnassignGlobals := noeval(ReadLibrary(Globals,UnassignGlobals)):

# Webtools, added by AS, June 6, 2006
ReadURL := noeval(ReadLibrary(WebTools,ReadURL)):
DownloadURL := noeval(ReadLibrary(WebTools,DownloadURL)):

# MST, added by CD, Dec 2006
MST := noeval(ReadLibrary(Graph,MST)):

# Center the "root" of unrooted trees.  AR, April 2007
CenterTreeRoot := noeval(ReadLibrary(CenterTreeRoot,CenterTreeRoot)):
TreeSize := noeval(ReadLibrary(CenterTreeRoot,TreeSize)):

ReadLibrary('Wrappers/wrapperinit'):

# Romberg, added by CD, Dec 2007
Romberg := noeval(ReadLibrary(Integrate)):

# UnionFind, added by AA, March 2008
UnionFind := noeval(ReadLibrary(UnionFind)):

# ConcatStrings, added by CD, May 2008
ConcatStrings := noeval(ReadLibrary(ConcatStrings)):
trim := noeval(ReadLibrary(StringManipulation, trim)):

# RobinsonFoulds, added by AA, Jul 2008
RobinsonFoulds := noeval(ReadLibrary(RobinsonFoulds)):
IntraDistance := noeval(ReadLibrary(IntraDistance)):
BipartiteSquared := noeval(ReadLibrary(BipartiteSquared)):

EvolutionaryOptimization := noeval(ReadLibrary(EvolutionaryOptimization)):
EvoMinimize := noeval(ReadLibrary(EvoMinimize)):
ProbabilisticFA := noeval(ReadLibrary(ProbabilisticFA)):
CompressedPFA := noeval(ReadLibrary(ProbabilisticFA,CompressedPFA)):
SparsePFA := noeval(ReadLibrary(ProbabilisticFA,SparsePFA)):

# RedoCompletion, added by CD, Aug 2008
RedoCompletion := noeval(ReadLibrary(RedoCompletion)):

# TaxonID - 5letter mapping
SpeciesCode := noeval(ReadLibrary(TaxTools, SpeciesCode)):
TaxonId := noeval(ReadLibrary(TaxTools, TaxonId)):
UpdateSpeciesCode := noeval(ReadLibrary(TaxTools, UpdateSpeciesCode)):
Tax2Five := noeval(ReadLibrary(TaxTools,Tax2Five)): # backward compatibility
Five2Tax := noeval(ReadLibrary(TaxTools,Five2Tax)): # backward compatibility

# PruneTree, added by AA, Jan 06, 2009
PruneTree := noeval(ReadLibrary(Tree, PruneTree)):

# ReconcileTree, added by AA, Jan 06, 2009
ReconcileTree := noeval(ReadLibrary(Reconcile,ReconcileTree)):

MLBranches := noeval(ReadLibrary(MLBranches)):

# Rank, added by AA, Feb 18. 2009
Rank := noeval(ReadLibrary(Rank, Rank)):
# cor, added by AA, Feb 18 2009
cor := noeval(ReadLibrary(Stat,cor)):

# MySql wrapper, added by AA, May 13, 2009
MySql := noeval(ReadLibrary(MySQL, MySql)):
MySqlResult := noeval(ReadLibrary(MySQL, MySqlResult)):

# BirthDeathTree, added by DD, May 26 2010
BirthDeathTree := noeval(ReadLibrary(BirthDeathTree, BirthDeathTree)):
ScaleTree := noeval(ReadLibrary(BirthDeathTree, ScaleTree)):
ScaleTreeLength := noeval(ReadLibrary(BirthDeathTree, ScaleTreeLength)):
AddDeviation := noeval(ReadLibrary(BirthDeathTree, AddDeviation)):

LoadMatrixFile := noeval(ReadLibrary(LoadMatrixFile, LoadMatrixFile)):
CreateCodonModelMatrices := noeval(ReadLibrary(YangModels, CreateCodonModelMatrices)):
CreateParametricQMatrix := noeval(ReadLibrary(YangModels, CreateParametricQMatrix)):
GammaRates := noeval(ReadLibrary(GammaRates)):

CreateNucleotideMatrices := noeval(ReadLibrary(NucleotideMatrix, CreateNucleotideMatrices)):
NucToNInt := noeval(ReadLibrary(NucleotideMatrix, NucToNInt)):
NIntToNuc := noeval(ReadLibrary(NucleotideMatrix, NIntToNuc)):
NucleotideMutate := noeval(ReadLibrary(NucleotideMatrix, NucleotideMutate)):

WriteSeqXML := noeval(ReadLibrary(DBConverters, WriteSeqXML)):
RenderTemplate := noeval(ReadLibrary(RenderTemplate, RenderTemplate)):

Graph_XGMML := noeval(ReadLibrary(Graph,Graph_XGMML)):
Tag := noeval(ReadLibrary(Tag,Tag)):
TagNV := noeval(ReadLibrary(Tag,TagNV)):
TagTable := noeval(ReadLibrary(Tag,TagTable)):

# KHTest by Wang Bo, Dec 2011
KHTest := noeval(ReadLibrary(KHTest, KHTest)):
ReadFastaIntoMAlignment := noeval(ReadLibrary(KHTest, ReadFastaIntoMAlignment)):
MLTopoTest := noeval(ReadLibrary(KHTest, MLTopoTest)):

# Ancestral Recombination Graph
ARG := noeval(ReadLibrary(AncestralRecombinationGraph)):
RecombinationNode := noeval(ReadLibrary(AncestralRecombinationGraph, RecombinationNode)):
CoalescentNode := noeval(ReadLibrary(AncestralRecombinationGraph, CoalescentNode)):
LeafNode := noeval(ReadLibrary(AncestralRecombinationGraph, LeafNode)):
GraphViz_ARG := noeval(ReadLibrary(AncestralRecombinationGraph, GraphViz_ARG)):

# Scientific Databases
SDB_Usage := noeval(ReadLibrary(SDB,SDB_Usage)):
SDB_Store := noeval(ReadLibrary(SDB,SDB_Store)):
SDB_StoreAttribute := noeval(ReadLibrary(SDB,SDB_StoreAttribute)):
SDB_Retrieve := noeval(ReadLibrary(SDB,SDB_Retrieve)):
SDB_RetrieveFile := noeval(ReadLibrary(SDB,SDB_RetrieveFile)):
SDB_EraseFile := noeval(ReadLibrary(SDB,SDB_EraseFile)):
SDB_Output := noeval(ReadLibrary(SDB,SDB_Output)):
SDB_Flush := noeval(ReadLibrary(SDB,SDB_Flush)):

MatchRegex := proc( pattern:string, txt:string) option builtin; 248 end:
ZmqRequest := proc( endpoint:string, msg:string) option builtin; 249 end:

TaxonomyEntry := noeval(ReadLibrary('Taxonomy',TaxonomyEntry)):
TaxonomyDownload := noeval(ReadLibrary('Taxonomy',TaxonomyDownload)):
json := noeval(ReadLibrary('json',json)):

DetectRepeats := noeval(ReadLibrary(DetectRepeats,DetectRepeats)):
DetectRepeatsInSeqs := noeval(ReadLibrary(DetectRepeats,DetectRepeatsInSeqs)):
WriteTreks := noeval(ReadLibrary(DetectRepeats,WriteTreks)):

